Publications


📚 Total Citations: 719
🧠 h-index: 7
🏆 i10-index: 7

Scientific papers

2025

  • Improving drug repositioning with negative data labeling using large language models
    M. Picard, M. Leclercq, A. Bodein, M.P. Scott-Boyer, O. Perin, A. Droit
    Journal of Cheminformatics, https://doi.org/10.1186/s13321-025-00962-0

2024

  • Target repositioning using multi-layer networks and machine learning: the case of prostate cancer
    M. Picard, M.P. Scott-Boyer, A. Bodein, M. Leclercq, J. Prunier, O. Perin, A. Droit
    Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2024.06.012

  • Combined transcriptomics and proteomics unveil the impact of vitamin C in modulating specific protein abundance in the mouse liver
    Aumailley, L., Bodein A., Adjibade, P. et al. 
    BMC Biological Research, https://doi.org/10.1186/s40659-024-00509-x

  • Proteomic Profiling of Samples Derived from a Murine Model Following Cryptococcus neoformans Infection
    Muselius B., A. Bodein, Roux-Dalvai F., Droit A., Geddes-McAlister J.
    Methods in Molecular Biology (Book chapter), https://doi.org/10.1007/978-1-0716-3722-7_9

  • SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated
    O. E. T. Bergum, A. H. Singleton, L. M. Røst, A. Bodein, M.-P. Scott-Boyer, M. B. Rye, A. Droit, P. Bruheim, M. Otterlei
    Frontiers in Microbiology, https://doi.org/10.3389/fmicb.2024.1373344

2023

  • Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment
    S. Lafleur\(^\star\), A. Bodein\(^\star\), J. M. M. Mutombo, A. Mathieu, C. Joly Beauparlant, X. Minne, F. Chandad, A. Droit, V. P. Houde

    International Journal of Molecular Sciences, https://doi.org/10.3390/ijms24108832

  • High dairy products intake modifies the correlation between α-tocopherol levels and serum proteins related to lipid metabolism in subjects at risk of type 2 diabetes
    A. Mahdavi, M. Leclercq, A. Bodein, C. Gotti, K. Greffard, J.F. Bilodeau, A. Droit, M. Lebel, I. Rudkowska
    Journal of Functional Foods, https://doi.org/10.1016/j.jff.2022.105375

  • Decoding Epidermis Reconstruction through Time-course Multi-omics Data Integration
    E. Bou Samra, C. Tacheau, M.P. Scott-Boyer, A. Bodein, A. Foucher, K. Abed, V. Segaud, F. Thillou, N. Boyera, N. Misra, A. Droit, O. Perin, N. Cavusoglu
    IFSCC Magazine, Volume 25(5), Winner of the Basic Research Award

2022

  • Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context
    V. Robin, A. Bodein, M.P. Scott-Boyer, M. Leclercq, O. Perin, A. Droit
    Frontiers in Molecular Biosciences, https://doi.org/10.3389/fmolb.2022.962799

  • The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation
    E. Doré, C. Joly-Beauparlant, S. Morozumi, A. Mathieu, T. Lévesque, I. Allaeys, AC. Duchez, N. Cloutier, M. Leclercq, A. Bodein, C. Payré, C. Martin, A. Petit-Paitel, M. H. Gelb, M. Rangachari, M. Murakami, L. Davidovic, N. Flamand, M. Arita, G. Lambeau, A. Droit, E. Boilard
    JCI Insight, https://doi.org/10.1172/jci.insight.152638

  • Interpretation of network-based integration from multi-omics longitudinal data
    A. Bodein, M.P. Scott-Boyer, O. Perin, K-A. Lê Cao, A. Droit
    Nucleic Acids Research, https://doi.org/10.1093/nar/gkab1200

  • timeOmics: an R package for longitudinal multi-omics data integration
    A. Bodein, M.P. Scott-Boyer, O. Perin, K-A. Lê Cao, A. Droit
    Bioinformatics, https://doi.org/10.1093/bioinformatics/btab664

2021

  • Integration strategies of multi-omics data for machine learning analysis
    M. Picard, M.P. Scott-Boyer, A. Bodein, O. Perin, A. Droit
    Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2021.06.030

2020

  • Adipose tissue transcriptome is related to pollutant exposure in polar bear mother-cub pairs from Svalbard, Norway
    P. Herst, J. Aars, C. Joly-Beauparlant, A. Bodein, M. Dalvai, D. Gagne, A. Droit, J. Bailey, H. Routti
    Environmental Science & Technology, https://doi.org/10.1021/acs.est.0c01920

2019

  • A generic multivariate framework for the integration of microbiome longitudinal studies with other data types
    A. Bodein, O. Chapleur, A. Droit, K-A. Lê Cao
    Frontiers in Genetics, https://doi.org/10.3389/fgene.2019.00963

R Packages

Talks

  • Integration of Microbiome and Multi-Omics Longitudinal Data
    A. Bodein , O. Chapleur, A. Droit, K-A. Lê Cao 2019 Presented to : 3 Workshop in Statistical Algorithms Challenges in Microbiome Data Analysis, New-York, USA

Posters

  • Prediction of Drug-Induced Liver Toxicity through Topological Motif Analysis in Protein Networks May 2025 D. Benyakhlaf, A. Bodein, A. Droit
    Presented to : Journées de la Recherche du CHU de Québec, Québec, Canada

  • Amélioration du repositionnement de médicaments avec l’étiquetage de données négatives grâce aux grands modèles de langage Mar. 2025
    M. Picard, M. Leclercq, A. Bodein, M.P. Scott-Boyer, O. Perin, A. Droit
    Presented to : Journée de l’Axe Endo-néphrologie, Québec, Canada

  • Tissue-specific network analysis to predict the hepatotoxicity of compounds Aug. 2023
    M.P. Scott-Boyer, A. Bodein, R. Grall, B. Ambroise, A. Riu, O. Perin, A. Droit
    Presented to : 12th World Congress on Alternatives and Animal Use in the Life Sciences, Niagara Falls, Canada

  • A framework to integrate multi-omics longitudinal dataset Sept. 2019
    M.P. Scott-Boyer, A. Bodein, K-A. Lê Cao, O. Perin, A. Droit
    Presented to : EMBO|EMBL - Multiomics to Mechanisms – Challenges in Data Integration, Heidelberg, Germany

  • Integration of Microbiome and Multi-Omics Longitudinal Data May 2019
    A. Bodein, O. Chapleur, A. Droit, K-A. Lê Cao
    Presented to : Journées de la Recherche du CHU de Québec, Québec, Canada

  • WHORMSS® : Taxonomic and functional exploration from metagenome shotgun sequencing July 2017
    Y. Laurent, J. Denonfoux, A. Bodein, S. Ferreira
    Presented to : Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Lille, France